#-c keep those that have unique alignment (Discard a MEM if it has more than INT occurence in the genome. This is an insensitive parameter. [10000])
#-r by reducing it to 1, I get bwa mem to work things out more intensively, like the --best command for bowtie (Larger value yields fewer seeds, which leads to faster alignment speed but lower accuracy)
#-k seed length (I thing that 32 is to big????)
#-M keep it compatible with picard tools
#-t threads to use

What are your opinion on the -c and -r strings?

then I get to see the produced file and it has sequences that are marked with the optional field of XA:Z and SA:Z